Is SETBP1 p.Pro696fs (c.2087del) pathogenic?

SETBP1 p.Pro696fs (c.2087del) is classified Pathogenic in SETBP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-24). No gnomAD frequency available for this variant; Associated with SETBP1-related disorder.

What condition is associated with SETBP1 p.Pro696fs (c.2087del)?

SETBP1 p.Pro696fs (c.2087del) is associated with SETBP1-related disorder (ClinVar).

How common is SETBP1 p.Pro696fs (c.2087del) in the general population?

SETBP1 p.Pro696fs (c.2087del) is no gnomAD frequency available for this variant (gnomAD).

SETBP1 p.Pro696fs

c.2087del · rs1568235567 · VCV2630876

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

SETBP1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 4 of 6
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.94	GERP 0.36, phastCons 0.006

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SETBP1
Protein: p.Pro696fs
Coding: c.2087del
MANE Select: NM_015559
dbSNP: rs1568235567
Type: Deletion
Location: chr18:44951423 (GRCh38)
Gene constraint: LOEUF 0.143 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 43.30

Full SETBP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

SETBP1-related disorder

Similar variants

SETBP1 p.Ala1071fs Pathogenic ★★ same condition
SETBP1 p.Pro696Gln Likely benign ★ same residue
SETBP1 p.Arg544Ter Pathogenic/Likely pathogenic ★★ same condition
SETBP1 p.Arg626Ter Pathogenic ★★ same condition
SETBP1 p.Asp868Asn Pathogenic ★★ ⚠ same condition
SETBP1 p.Ser867Arg Pathogenic/Likely pathogenic ★★ ⚠ same condition
SETBP1 p.Lys664Glu Uncertain significance ★★ ⚠ same condition
SETBP1 p.Gln712Ter Pathogenic ★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/setbp1-p-pro696fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown